MolNFT v1 · #85085 · protein

Ykud L,D-transpeptidase from B.SUBTILIS

4A1J · Putative L, D-transpeptidase ykud: “Ykud L,D-transpeptidase from B.SUBTILIS”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.76). MolNFT v1 #85085 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4A1J
Type: protein
Length: 330 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative L, D-transpeptidase ykud
EC: 2.-.-.-
UniProt: O34816
Ligands: SO4
Pockets: 3 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 20% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Putative L, D-transpeptidase ykud (EC 2.-.-.-)	protein	165	20% helix, 35% strand	O34816

Ligands and binding sites

SO4 · Sulfate ion · ion · 6 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	631	0.76	0.82	85	SO4
2	221	0.47	0.74	34	SO4
3	111	0.46	0.79	21	SO4

Interfaces

1 interface between chains.

A–B · 673 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

4A1J · Ykud L,D-transpeptidase from B.subtilis · the same entry in another collection · chain A against A, TM-score 1.00
O34816 · AlphaFold monomer V2.0 prediction for putative L,D-transpeptidase ykud (O34816) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O34816
Elsewhere: RCSB PDB 4A1J · PDBe 4A1J · UniProt O34816

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